Tag Archives: synthetic molecules

Unlock a computer with information encoded in a synthetic molecule

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A May 16, 2025 news item on ScienceDaily announced a new (albeit expensive) method for using passwords,

Molecules like DNA are capable of storing large amounts of data without requiring an energy source, but accessing this molecular data is expensive and time consuming. Publishing May 16 [2025] in the Cell Press journal Chem, researchers have developed an alternative method to encode information in synthetic molecules, which they used to encode and then decode an 11-character password to unlock a computer.

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Caption: Message encoded in a molecule Credit: Pandey et al., Chem License: CC BY-SA

A May 16, 2025 Cell Press press release on EurekAlert, which originated the news item, provides more detail,

“Molecules can store information for very long periods without needing power. Nature has given us the proof of principle that this works,” says corresponding author and electrical engineer Praveen Pasupathy of the University of Texas at Austin. “This is the first attempt to write information in a building block of a plastic that can then be read back using electrical signals, which takes us a step closer to storing information in an everyday material.”  

Traditional storage devices like hard drives and flash drives have drawbacks, such as high maintenance costs, energy consumption, and short lifespans that make them unsuitable for long-term data archiving. Molecules could provide an alternative option, and prior studies have shown that DNA and synthetic polymers can be designed to effectively store information. However, decoding these molecules usually involves expensive pieces of equipment, for example, mass spectrometers.  

To make molecular messages that are easier to write and read, the team decided to try a different approach: designing molecules that contain electrochemical information—a method that allows messages to be decoded using electrical signals. 

“Our approach has the potential to be scaled down to smaller, more economical devices compared to traditional spectrometry-based systems,” says senior author and chemist Eric Anslyn of the University of Texas at Austin. “It opens exciting prospects for interfacing chemical encoding with modern electronic systems and devices.” 

To start, the team built an alphabet of characters using four different monomers, or molecular building blocks with different electrochemical properties. Each character was composed of different combinations of the four monomers, which yielded a total of 256 possible characters. To test the method, they used the molecular alphabet to synthesize a chain-like polymer representing an 11-character password (‘Dh&@dR%P0W¢’), which they subsequently decoded using a method based on the molecules’ electrochemical properties. 

The team’s decoding method takes advantage of the fact that certain chain-like polymers can be broken down by removing one building block at a time from the end of the chain. Since the monomers were designed to have unique electrochemical properties, this step-by-step degradation results in electrical signals that can be used to decipher the sequential identity of the monomers within the polymer. 

“The voltage gives you one piece of information —the identity of the monomer currently being degraded—and so we scan through different voltages and watch this movie of the molecule being broken down, which tells us which monomer is being degraded at which point in time,” says Pasupathy. “Once we pinpoint which monomers are where, we can piece that together to get the identities of the characters in our encoded alphabet.” 

One downside of the method is that each molecular message can only be read once, since decoding the polymers involves degrading them. The decoding process also takes time—around 2.5 hours for the 11-character password—but the team are working on methods to speed up the process. 

“While this method does not yet overcome the destructive or time-intensive aspects of sequencing, it takes a first step toward the ultimate goal of developing portable, integrated technologies for polymer-based data storage,” says Anslyn. “The next step is to interface the polymers with integrated circuits, where the computer chips become the readout system for the stored information.” 

Here’s a link to and a citation for the paper,

Electrochemical sequencing of sequence-defined ferrocene-containing oligourethanes by Bipin Pandey, Bharadwaj Muralidharan, Tianmu Ma, Akshi Pant, Matthew Onorato, Kenneth A. Johnson, Ananth Dodabalapur, Praveen Pasupathy, Eric V. Anslyn. Chem, 2025; 102571 DOI: 10.1016/j.chempr.2025.102571

This paper is behind a paywall.

Sugar in your bones might be better for you than you think

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These days sugar is often  viewed as leading to health problems but there is an instance where it may be useful—bone regeneration. From a June 19, 2017 news item on Nanowerk (Note: A link has been removed),

There hasn’t been a gold standard for how orthopaedic spine surgeons promote new bone growth in patients, but now Northwestern University scientists have designed a bioactive nanomaterial that is so good at stimulating bone regeneration it could become the method surgeons prefer.

While studied in an animal model of spinal fusion, the method for promoting new bone growth could translate readily to humans, the researchers say, where an aging but active population in the U.S. is increasingly receiving this surgery to treat pain due to disc degeneration, trauma and other back problems. Many other procedures could benefit from the nanomaterial, ranging from repair of bone trauma to treatment of bone cancer to bone growth for dental implants.

“Regenerative medicine can improve quality of life by offering less invasive and more successful approaches to promoting bone growth,” said Samuel I. Stupp, who developed the new nanomaterial. “Our method is very flexible and could be adapted for the regeneration of other tissues, including muscle, tendons and cartilage.”

Stupp is director of Northwestern’s Simpson Querrey Institute for BioNanotechnology and the Board of Trustees Professor of Materials Science and Engineering, Chemistry, Medicine and Biomedical Engineering.

For the interdisciplinary study, Stupp collaborated with Dr. Wellington K. Hsu, associate professor of orthopaedic surgery, and Erin L. K. Hsu, research assistant professor of orthopaedic surgery, both at Northwestern University Feinberg School of Medicine. The husband-and-wife team is working to improve clinically employed methods of bone regeneration.

Sugar molecules on the surface of the nanomaterial provide its regenerative power. The researchers studied in vivo the effect of the “sugar-coated” nanomaterial on the activity of a clinically used growth factor, called bone morphogenetic protein 2 (BMP-2). They found the amount of protein needed for a successful spinal fusion was reduced to an unprecedented level: 100 times less of BMP-2 was needed. This is very good news, because the growth factor is known to cause dangerous side effects when used in the amounts required to regenerate high-quality bone, and it is expensive as well.

A June 19, 2017 Northwestern University news release by Megan Fellman, which originated the news item, tells the rest of the story,

Stupp’s biodegradable nanomaterial functions as an artificial extracellular matrix, which mimics what cells in the body usually interact with in their surroundings. BMP-2 activates certain types of stem cells and signals them to become bone cells. The Northwestern matrix, which consists of tiny nanoscale filaments, binds the protein by molecular design in the way that natural sugars bind it in our bodies and then slowly releases it when needed, instead of in one early burst, which can contribute to side effects.

To create the nanostructures, the research team led by Stupp synthesized a specific type of sugar that closely resembles those used by nature to activate BMP-2 when cell signaling is necessary for bone growth. Rapidly moving flexible sugar molecules displayed on the surface of the nanostructures “grab” the protein in a specific spot that is precisely the same one used in biological systems when it is time to deploy the signal. This potentiates the bone-growing signals to a surprising level that surpasses even the naturally occurring sugar polymers in our bodies.

In nature, the sugar polymers are known as sulfated polysaccharides, which have super-complex structures impossible to synthesize at the present time with chemical techniques. Hundreds of proteins in biological systems are known to have specific domains to bind these sugar polymers in order to activate signals. Such proteins include those involved in the growth of blood vessels, cell recruitment and cell proliferation, all very important biologically in tissue regeneration. Therefore, the approach of the Stupp team could be extended to other regenerative targets.

Spinal fusion is a common surgical procedure that joins adjacent vertebra together using a bone graft and growth factors to promote new bone growth, which stabilizes the spine. The bone used in the graft can come from the patient’s pelvis — an invasive procedure — or from a bone bank.

“There is a real need for a clinically efficacious, safe and cost-effective way to form bone,” said Wellington Hsu, a spine surgeon. “The success of this nanomaterial makes me excited that every spine surgeon may one day subscribe to this method for bone graft. Right now, if you poll an audience of spine surgeons, you will get 15 to 20 different answers on what they use for bone graft. We need to standardize choice and improve patient outcomes.”

In the in vivo portion of the study, the nanomaterial was delivered to the spine using a collagen sponge. This is the way surgeons currently deliver BMP-2 clinically to promote bone growth.

The Northwestern research team plans to seek approval from the Food and Drug Administration to launch a clinical trial studying the nanomaterial for bone regeneration in humans.

“We surgeons are looking for optimal carriers for growth factors and cells,” Wellington Hsu said. “With its numerous binding sites, the long filaments of this new nanomaterial is more successful than existing carriers in releasing the growth factor when the body is ready. Timing is critical for success in bone regeneration.”

In the new nanomaterial, the sugars are displayed in a scaffold built from self-assembling molecules known as peptide amphiphiles, first developed by Stupp 15 years ago. These synthetic molecules have been essential in his work on regenerative medicine.

“We focused on bone regeneration to demonstrate the power of the sugar nanostructure to provide a big signaling boost,” Stupp said. “With small design changes, the method could be used with other growth factors for the regeneration of all kinds of tissues. One day we may be able to fully do away with the use of growth factors made by recombinant biotechnology and instead empower the natural ones in our bodies.”

Here’s a link to and a citation for the paper,

Sulfated glycopeptide nanostructures for multipotent protein activation by Sungsoo S. Lee, Timmy Fyrner, Feng Chen, Zaida Álvarez, Eduard Sleep, Danielle S. Chun, Joseph A. Weiner, Ralph W. Cook, Ryan D. Freshman, Michael S. Schallmo, Karina M. Katchko, Andrew D. Schneider, Justin T. Smith, Chawon Yun, Gurmit Singh, Sohaib Z. Hashmi, Mark T. McClendon, Zhilin Yu, Stuart R. Stock, Wellington K. Hsu, Erin L. Hsu, & Samuel I. Stupp. Nature Nanotechnology 12, 821–829 (2017) doi:10.1038/nnano.2017.109 Published online 19 June 2017

This paper is behind a paywall.